It is failing and you aren't getting an error message. Maybe you will
see something if you run interactively.
In the absence of more info, I would try with a simple min.in - if that
fails too, then there is likely a problem with your model.
I think restraints in min are more trouble than they are worth, unless
you are consciously sculpting something.
Bill
On 6/28/17 12:53 PM, Sumudu Leelananda wrote:
> Nope.
>
> This is all I get:
>
>
> -------------------------------------------------------
> Amber 14 SANDER 2014
> -------------------------------------------------------
>
> | Run on 06/28/2017 at 10:47:03
>
> | Executable path: sander.MPI
> | Working directory: /tmp/pbstmp.9464152
> | Hostname: n0122.ten.osc.edu
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: step2_min0.in
>
> | MDOUT: step2_min0.out
>
> |INPCRD: protein_1CA6.inpcrd
>
> | PARM: protein_1CA6.prmtop
>
> |RESTRT: step2_min0.rst
>
> | REFC: protein_1CA6.inpcrd
>
> | MDVEL: mdvel
>
> | MDFRC: mdfrc
>
> | MDEN: mden
>
> | MDCRD: mdcrd
>
> |MDINFO: mdinfo
>
> | MTMD: mtmd
>
> |INPDIP: inpdip
>
> |RSTDIP: rstdip
>
> |INPTRA: inptraj
>
>
> | REMLOG: rem.log
> | REMTYPE: rem.type
> | REMSTRIP:
> | SAVEENE: saveene
> |CLUSTERINF: cluster.info
> | RESERVOIR: reserv/frame
> | REMDDIM:
>
>
> Here is the input file:
>
> System minimization:
>
> &cntrl
>
> imin=1, ntmin=2, nmropt=0, drms=0.1
>
> maxcyc=20000, ncyc=1500,
>
> ntx=1, irest=0,
>
> ntpr=500, ntwr=500, ntwx=500, iwrap=1,
>
> ntf=1, ntb=1, cut=10.0, nsnb=20,
>
> ntc=1,
>
> icfe = 1, ifsc = 0,
>
> clambda=0.5,
>
> ioutfm=1,
>
> nmropt=1/
>
> &wt type='DUMPFREQ', istep1=500, /
>
> &wt type='END', /
>
> DISANG=rest_step2.in
>
> DUMPAVE=rest.txt
>
> LISTIN=POUT
>
> LISTOUT=POUT /
>
> &end
>
>
>
>
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> | Flags: MPI
>
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info found
> |Largest sphere to fit in unit cell has radius = 33.907
> | New format PARM file being parsed.
> | Version = 1.000 Date = 04/14/17 Time = 10:45:04
> NATOM = 25384 NTYPES = 16 NBONH = 24666 MBONA = 711
> NTHETH = 1538 MTHETA = 960 NPHIH = 2969 MPHIA = 2332
> NHPARM = 0 NPARM = 0 NNB = 39532 NRES = 8103
> NBONA = 711 NTHETA = 960 NPHIA = 2332 NUMBND = 30
> NUMANG = 61 NPTRA = 33 NATYP = 25 NPHB = 1
> IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 2143344
> | Hollerith 84257
> | Integer 856534
> | Max Pairs 1624576
> | nblistReal 304608
> | nblist Int 878284
> | Total 32576 kbytes
>
> | Note: 1-4 EEL scale factors are being read from the topology file.
>
> | Note: 1-4 VDW scale factors are being read from the topology file.
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> BOX TYPE: RECTILINEAR
>
>
> On Wed, Jun 28, 2017 at 3:51 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> Do you see energies being printed every 500 steps in the .out file?
>>
>> Bill
>>
>>
>> On 6/28/17 12:47 PM, Sumudu Leelananda wrote:
>>> This is Step2_min0.in
>>>
>>> I will try without mpi as well. Thank you.
>>>
>>> System minimization:
>>> &cntrl
>>> imin=1, ntmin=2, nmropt=0, drms=0.1
>>> maxcyc=20000, ncyc=1500,
>>> ntx=1, irest=0,
>>> ntpr=500, ntwr=500, ntwx=500, iwrap=1,
>>> ntf=1, ntb=1, cut=10.0, nsnb=20,
>>> ntc=1,
>>> icfe = 1, ifsc = 0,
>>> clambda=0.5,
>>> ioutfm=1,
>>> nmropt=1/
>>> &wt type='DUMPFREQ', istep1=500, /
>>> &wt type='END', /
>>> DISANG=rest_step2.in
>>> DUMPAVE=rest.txt
>>> LISTIN=POUT
>>> LISTOUT=POUT /
>>> &end
>>>
>>>
>>>
>>> On Wed, Jun 28, 2017 at 3:43 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>
>>>> Please paste step2_min0.in here.
>>>>
>>>> Also, you might try without mpi.
>>>>
>>>> Bill
>>>>
>>>>
>>>> On 6/28/17 12:29 PM, Sumudu Leelananda wrote:
>>>>> I could not find any errors in that out file... Any hints?
>>>>>
>>>>> Thank you!
>>>>>
>>>>> On Wed, Jun 28, 2017 at 3:08 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>>>
>>>>>> Look at step2_min0.out for clues as to why the rst wasn't generated.
>>>>>>
>>>>>> Bill
>>>>>>
>>>>>>
>>>>>> On 6/28/17 12:05 PM, Sumudu Leelananda wrote:
>>>>>>> Dear Dr. Loeffler
>>>>>>>
>>>>>>> Thank you for your suggestion. I tried it but it still gives the same
>>>>>> error:
>>>>>>> Error opening unit 30: File "step2_min0.rst" is missing or
>> unreadable
>>>>>>> I attached the inputs and also the output files for the charge step.
>>>>>>>
>>>>>>> mpiexec sander.MPI -O -i step2_min0.in -o step2_min0.out -c
>>>>>>> protein_1CA6.inpcrd -p protein_1CA6.prmtop -r step2_min0.rst -ref
>>>>>>> protein_1CA6.inpcrd
>>>>>>>
>>>>>>> mpiexec sander.MPI -O -i step2_min1.in -o step2_min1.out -c
>>>>>>> protein_1CA6.inpcrd -p protein_1CA6.prmtop -r step2_min1.rst -ref
>>>>>>> protein_1CA6.inpcrd
>>>>>>>
>>>>>>> mpiexec sander.MPI -O -i step2_heat0.in -o step2_heat0.out -c
>>>>>>> step2_min0.rst -p protein_1CA6.prmtop -r step2_heat0.rst -x
>>>>>> step2_heat0.nc
>>>>>>> -ref step2_min0.rst
>>>>>>>
>>>>>>> mpiexec sander.MPI -O -i step2_heat1.in -o step2_heat1.out -c
>>>>>>> step2_min1.rst -p protein_1CA6.prmtop -r step2_heat1.rst -x
>>>>>> step2_heat1.nc
>>>>>>> -ref step2_min1.rst
>>>>>>>
>>>>>>> mpiexec sander.MPI -O -i step2_md0.in -o step2_md0.out -c
>>>>>> step2_heat0.rst
>>>>>>> -p protein_1CA6.prmtop -r step2_md0.rst -x step2_md0.nc -ref
>>>>>> step2_heat0.rst
>>>>>>> mpiexec sander.MPI -O -i step2_md1.in -o step2_md1.out -c
>>>>>> step2_heat1.rst
>>>>>>> -p protein_1CA6.prmtop -r step2_md1.rst -x step2_md1.nc -ref
>>>>>> step2_heat1.rst
>>>>>>> Could you please give me suggestions or hints on this?
>>>>>>>
>>>>>>> Also, according to what you suggested it seems like we don't need a
>>>>>>> restraint step when doing Sander? I can just only have the charge
>>>> removal
>>>>>>> step [2] and the van der Waals forces removal step [3]. Is that
>> right?
>>>>>>> Thank you!
>>>>>>>
>>>>>>> On Wed, Jun 28, 2017 at 12:18 PM, Sumudu Leelananda <
>>>>>>> sumudu.leelananda.gmail.com> wrote:
>>>>>>>
>>>>>>>> Dear Dr. Loeffler
>>>>>>>>
>>>>>>>> Thank you for your suggestion. I tried it but it still gives the
>> same
>>>>>>>> error:
>>>>>>>>
>>>>>>>> Error opening unit 30: File "step2_min0.rst" is missing or
>>>> unreadable
>>>>>>>> I attached the inputs and also the output files for the charge step.
>>>>>>>>
>>>>>>>> Could you please give me suggestions on this?
>>>>>>>>
>>>>>>>> Also, according to what you suggested it seems like we don't need a
>>>>>>>> restraint step when doing Sander? I can just only have the charge
>>>>>> removal
>>>>>>>> step [2] and the van der Waals forces removal step [3]. Is that
>> right?
>>>>>>>> Thank you!
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, Jun 2, 2017 at 3:19 AM, Hannes Loeffler <
>>>>>>>> Hannes.Loeffler.stfc.ac.uk> wrote:
>>>>>>>>
>>>>>>>>> On Thu, 1 Jun 2017 15:22:53 -0400
>>>>>>>>> Sumudu Leelananda <sumudu.leelananda.gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Dear Hannes
>>>>>>>>>>
>>>>>>>>>> Thank you for your reply. I'm sorry, I only got a part of your
>>>> reply
>>>>>>>>>> and don't see the full reply on the archives yet. Yes. I'm using a
>>>>>>>>>> similar multisite Calcium model but the number of dummy atoms is
>>>>>>>>>> different than Sept Model you provided the link to.
>>>>>>>>>>
>>>>>>>>>> In PEMED I had 2 Ca ions in the restraint step (residue numbers 90
>>>>>>>>>> and 91). What I do is restraint 90 at the end of the restraint
>> step.
>>>>>>>>>> Then in the charge step remove the charge from 91 and in the vdW
>>>> step
>>>>>>>>>> totally remove 91. PEMED calculations worked without any issues.
>>>>>>>>>> Issues arise for Sander.
>>>>>>>>> So step 2 would be
>>>>>>>>> icfe = 1, ifsc = 0,
>>>>>>>>> timask1 = ':90', timask2 = ':91',
>>>>>>>>> crgmask = ':91'
>>>>>>>>>
>>>>>>>>> And step 3
>>>>>>>>> icfe = 1, ifsc = 1, scalpha = 0.5,
>>>>>>>>> timask1 = ':90', timask2 = '',
>>>>>>>>> scmask1 = ':90', scmask2 = ''
>>>>>>>>> crgmask = ':90'
>>>>>>>>>
>>>>>>>>> Step 3 obviously implies that you don't have a residue 91.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> In Sander which I'm doing now, I didn't see the need to have two
>>>>>>>>>> copies like that so I only have 90.
>>>>>>>>> Sander needs two topology files and two input files, and it doesn't
>>>>>> have
>>>>>>>>> timask.
>>>>>>>>>
>>>>>>>>> So 2a:
>>>>>>>>> icfe = 1, ifsc = 0,
>>>>>>>>>
>>>>>>>>> and 2b
>>>>>>>>> icfe = 1, ifsc = 0,
>>>>>>>>> crgmask = ':90'
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 3a:
>>>>>>>>> icfe = 1, ifsc = 1, scalpha = 0.5,
>>>>>>>>> scmask = ':90'
>>>>>>>>> crgmask = ':90'
>>>>>>>>>
>>>>>>>>> 3b:
>>>>>>>>> icfe = 1, ifsc = 1, scalpha = 0.5,
>>>>>>>>> scmask = ''
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
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Received on Wed Jun 28 2017 - 13:00:06 PDT
